pipeLIMMA: A pipeline for LIMMA.

Description Usage Arguments Details Value Examples

View source: R/pipeLIMMA.R

Description

pipeLIMMA Run a pipeline of LIMMA functions for differential gene expression.

Usage

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pipeLIMMA(counts, info, formula = NULL, contrast.matrix = NULL,
  block = NULL, design = NULL, runVoom = TRUE,
  use.qualityWeights = TRUE, use.topTable = FALSE, geneIDs = NA,
  verbose = TRUE, plotVoom = FALSE, ...)

Arguments

counts

A count matrix

info

An experimental design matrix

formula

A character string that can be coerced to a formula. Specify if a contrast model is not desired.

contrast.matrix

A matrix of contrasts, usually created by a call from limma:makeContrasts. Used only when limma:contrast.fit is intended as the statistical modeling function. NULL values force a traditional test of effects via limma::lmFit/ebayes.

block

A string that represents an individual that was repeatedly measured, if NULL, runs the analysis without a blocking / duplicate correlation factor

design

A design matrix, usually created by a call from "model.matrix". Used only if limma:contrast.fit is intended as the statistical modeling function. NULL values force a traditional test of effects via limma::lmFit/ebayes.

runVoom

Logical, if TRUE, normalizes the counts matrix via voom. If FALSE, assumes the counts matrix is already voom-normalized. Pre-running voom will speed up analyses with multiple pipeLIMMA calls.

use.qualityWeights

Logical, run voom with quality weights or not?

use.topTable

Logical, report F-statistics across all factors? If true, a third element is returned called fstats.

geneIDs

The names of genes. If NA, use row names from counts matrix

verbose

Logical, return progress updates?

plotVoom

Logical, plot the voom fit? Defaults to FALSE

...

additional arguments, not currently in use.

Details

This function runs the following pipeline:

Value

a list with 2 elements (if simple=TRUE)

Examples

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## Not run: 
data(kidney) # from simseq
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-data.frame(rep=kidney$replic,
                 treatment=kidney$treatment)
stats<-pipeLIMMA(counts=counts,
                 info=info,
                 formula = " ~ treatment",
                 block=info$rep)
stats<-pipeLIMMA(counts=counts,
                 info=info,
                 formula = " ~ treatment",
                 block=NULL)

## End(Not run)

jtlovell/deTools documentation built on Sept. 27, 2017, 10 a.m.